tetano
Editor, Senior Moderator
Arch Virol
. 2023 May 8;168(6):156.
doi: 10.1007/s00705-023-05787-6. Consensus insertion/deletions and amino acid variations of all coding and noncoding regions of the SARS-CoV-2 Omicron clades, including the XBB and BQ.1 lineages
Hamong Suharsono[SUP] 1 [/SUP], Bayu K Mahardika[SUP] 2 [/SUP], Putu H Sudipa[SUP] 3 [/SUP], Tri K Sari[SUP] 4 [/SUP], Ida B K Suardana[SUP] 4 [/SUP], Gusti N Mahardika[SUP] 5 6 [/SUP]
Affiliations
The currently dominant Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has swiftly diverged into clades. To predict the probable impact of these clades, the consensus insertions/deletions (indels) and amino acid substitutions of the whole genome of clades were compared with the original SARS-CoV-2 strain. The evolutionary history of representatives of clades and lineages was inferred using the maximum-likelihood method and tested using the bootstrap method. The indels and polymorphic amino acids were found to be either clade-specific or shared among clades. The 21K clade has unique indels and substitutions, which probably represent reverted indels/substitutions. Three variations that appear to be associated with SARS-CoV-2 attenuation in the Omicron clades included a deletion in the nucleocapsid gene, a deletion in the 3'untranslated region, and a truncation in open reading frame 8. Phylogenetic analysis showed that the Omicron clades and lineages form three separate clusters.
. 2023 May 8;168(6):156.
doi: 10.1007/s00705-023-05787-6. Consensus insertion/deletions and amino acid variations of all coding and noncoding regions of the SARS-CoV-2 Omicron clades, including the XBB and BQ.1 lineages
Hamong Suharsono[SUP] 1 [/SUP], Bayu K Mahardika[SUP] 2 [/SUP], Putu H Sudipa[SUP] 3 [/SUP], Tri K Sari[SUP] 4 [/SUP], Ida B K Suardana[SUP] 4 [/SUP], Gusti N Mahardika[SUP] 5 6 [/SUP]
Affiliations
- PMID: 37155081
- DOI: 10.1007/s00705-023-05787-6
The currently dominant Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has swiftly diverged into clades. To predict the probable impact of these clades, the consensus insertions/deletions (indels) and amino acid substitutions of the whole genome of clades were compared with the original SARS-CoV-2 strain. The evolutionary history of representatives of clades and lineages was inferred using the maximum-likelihood method and tested using the bootstrap method. The indels and polymorphic amino acids were found to be either clade-specific or shared among clades. The 21K clade has unique indels and substitutions, which probably represent reverted indels/substitutions. Three variations that appear to be associated with SARS-CoV-2 attenuation in the Omicron clades included a deletion in the nucleocapsid gene, a deletion in the 3'untranslated region, and a truncation in open reading frame 8. Phylogenetic analysis showed that the Omicron clades and lineages form three separate clusters.